TESK1

testis associated actin remodelling kinase 1, the group of MicroRNA protein coding host genes|LIMK/TESK kinase family

Basic information

Region (hg38): 9:35605262-35610041

Links

ENSG00000107140 ∙ NCBI:7016 ∙ OMIM:601782 ∙ HGNC:11731 ∙ Uniprot:Q15569 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TESK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TESK1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in TESK1

This is a list of pathogenic ClinVar variants found in the TESK1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-35605988-G-T		not specified	Uncertain significance (Sep 22, 2023)
9-35606936-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-35607352-G-A		not specified	Likely benign (Apr 13, 2022)
9-35607613-G-A		not specified	Uncertain significance (May 30, 2023)
9-35608187-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
9-35608405-G-A		not specified	Uncertain significance (Feb 22, 2023)
9-35608437-C-G		not specified	Uncertain significance (Mar 19, 2024)
9-35608443-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-35608870-G-A		not specified	Uncertain significance (Dec 28, 2023)
9-35608882-C-T		not specified	Uncertain significance (Jul 06, 2021)
9-35608967-C-G		not specified	Uncertain significance (Sep 27, 2021)
9-35608973-G-C		not specified	Uncertain significance (Jun 28, 2022)
9-35609065-G-A		not specified	Uncertain significance (Jun 02, 2023)
9-35609126-C-T		not specified	Uncertain significance (Jun 18, 2024)
9-35609162-G-A		not specified	Uncertain significance (Apr 01, 2022)
9-35609168-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-35609188-G-A		not specified	Uncertain significance (May 30, 2024)
9-35609221-G-A		not specified	Uncertain significance (Aug 16, 2021)
9-35609230-C-T		not specified	Uncertain significance (Feb 14, 2023)
9-35609291-C-T		not specified	Uncertain significance (May 25, 2022)
9-35609332-G-T		not specified	Uncertain significance (Dec 02, 2022)
9-35609348-T-C		not specified	Uncertain significance (Nov 16, 2021)
9-35609363-C-T		not specified	Uncertain significance (Jul 09, 2021)
9-35609398-G-A		not specified	Uncertain significance (Jun 18, 2021)
9-35609411-A-G		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TESK1	protein_coding	protein_coding	ENST00000336395	10	4672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00745	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	291	379	0.768	0.0000230	3931
Missense in Polyphen		62	141.64	0.43774		1485
Synonymous	0.819	147	160	0.918	0.00000941	1449
Loss of Function	4.36	3	27.9	0.108	0.00000177	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000589	0.0000589
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.00	0.00
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000452	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual specificity protein kinase activity catalyzing autophosphorylation and phosphorylation of exogenous substrates on both serine/threonine and tyrosine residues. Probably plays a central role at and after the meiotic phase of spermatogenesis (By similarity). {ECO:0000250}.
• Pathway: Regulation of cytoskeletal remodeling and cell spreading by IPP complex components;Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.142
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.704
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tesk1

Gene ontology

• Biological process: spermatogenesis;peptidyl-tyrosine phosphorylation;actin cytoskeleton organization;negative regulation of protein autophosphorylation;regulation of protein localization;positive regulation of stress fiber assembly;negative regulation of protein serine/threonine kinase activity
• Cellular component: nucleus;cytoplasm;cytosol;cytoplasmic vesicle
• Molecular function: protein serine/threonine kinase activity;protein serine/threonine/tyrosine kinase activity;protein tyrosine kinase activity;protein binding;ATP binding;protein C-terminus binding;protein kinase binding;metal ion binding